The Western Pacific Warm Pool (WPWP) is a region of great importance to the climate and ocean systems. Here, the highest sea surface temperature (SST) worldwide creates deep atmospheric convection that is regarded as the engine of the present-day atmospheric circulation and home to many climate phenomena such as tropical cyclones, monsoon and El Niño-Southern Oscillation (ENSO). The thermocline depth of the New Guinea Coastal Undercurrent (NGCUC) is the only cross-equatorial western boundary current connecting the South Pacific to the WPWP region that modulates the mass and heat balances of the WPWP and the ventilation of the equatorial Pacific thermocline. For that reason, the motivation exists for targeting the WPWP thermocline and NGCUC signal recorded in two sediment cores off the coast of northern Papua New Guinea (PNG) in order to determine the main controlling factor of WPWP thermocline depth and NGCUC variations during the late Holocene. To this end, we reconstruct the upper ocean hydrography using Mg/Ca-based temperature estimates of mixed-layer- (Globigerinoides ruber) and thermocline-dwelling planktic foraminifera (Pulleniatina obliquiloculata, Neoglobigerina dutertrei and Globorotalia tumida). The differences in stable Mg/Ca‐based temperatures (DT°C) of mixed-layer-dwelling and thermocline‐dwelling planktic foraminifera, which is a qualitative estimate for the state of the upper ocean thermal gradient and allows to reconstruct the upper water column structure, i.e. the depth of the thermocline. The Mg/Ca-based thermal gradient (ΔT) estimates reveal a prominent thermocline shoaling and shallower NGCUC after ~1500 yr BP. Our thermocline reconstructions suggest a highly active, El Niño-dominated climate regime after ~1500 yr BP.